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Showing posts from 2015

Now HIRING! Looking for passionate graduate students and post doctoral fellows

My group is currently recruiting people to fill two graduate student positions. We will also be recruiting a researcher to fill a postdoctoral position in the coming year.

We are looking for candidates who are passionate about genetics, genomics, and research. Ideal candidates are creative, hard working (while maintaining a work/life balance), and self starters. Our group is strictly computational, so candidates should enjoy working on computers and analyzing data. Candidates should be willing to learn programming (typically in R or Python), or already have some programming experience.

We will soon have access to over 200,000 genotyped beef cattle with phenotypes and breeding values. We also have access to whole genome sequencing data from over 2,000 cattle. So, if you like working with lots of data, come join us! Our group uses population genomics to better understand the  history of cattle breeds and to inform future selection decisions. We are interested in local genetic adaption, …

GENOMICS: Where are we going?

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The June/July issue of the Charolais Journal contained an article I wrote.

Click this link to download a copy of the article.

In the article I discuss trends I see coming in the development of genomic prediction. Please provide feedback in the anonymous survey below.


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Pigs that are Resistant to Incurable Disease Developed at University of Missouri

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Discovery about PRRS virus could save swine industry hundreds of millions of dollars; Exclusive deal signed with global leader in animal genetics COLUMBIA, Mo. ­— Porcine Reproductive and Respiratory Syndrome (PRRS) virus was first detected in the U.S. in 1987. Pigs that contract the disease have extreme difficulty reproducing, don’t gain weight and have a high mortality rate. To date, no vaccine has been effective, and the disease costs North American farmers more than $660 million annually. Now, a team of researchers from the University of Missouri, Kansas State University, and Genus plc have bred pigs that are not harmed by the disease.


Prather PRRS from MU News Bureau on Vimeo.


“Once inside the pigs, PRRS needs some help to spread; it gets that help from a protein called CD163,” said Randall Prather, distinguished professor of animal sciences in the College of Agriculture, Food and Natural Resources. “We were able to breed a litter of pigs that do not produce this protein, and as …

North American Limousin Foundation Releases Recalibrated GE-EPDs

By Joe Epperly, NALF assistant executive director

Limousin breeders and their commercial customers benefit greatly from new breeding and selection tools. The North American Limousin Foundation (NALF) has launched genomic-enhanced EPDs (GE-EPDs) with the fall 2015 international cattle evaluation. This provides GE-EPDs for all Limousin and Lim-Flex® animals that have completed DNA testing for genomic profiles.
A recalibration in cooperation with GeneSeek® and the Canadian Limousin Association has supplied genomic profiles on more than 4,500 Limousin and Lim-Flex animals. Molecular breeding values from either a high- or low-density genomic profile test are then blended into EPD calculations to produce GE-EPDs. This recalibration has led to the doubling of the number of animals included, the number of traits enhanced, and the genetic correlations.
The advantage to animals with GE-EPDs is increasing EPD accuracy values on many traits equivalent to having 8-20 progeny. This adds greatly to …

Heifer Sale Exceeds Expectations

by Eldon Cole, Livestock Specialist Headquartered in Lawrence County, MO
The skidding cattle market the past few months resulted in considerable pessimism prior to the 33rd Show-Me-Select (SMS) Bred Heifer Sale at Joplin Regional Stockyards on November 20.  However, when the last of 293 heifers left the ring, the average price of $2477 brought smiles to most of the sellers.
The previous 32 sales results predicted an average heifer price just under $2000 per head.  That forecast is based on the week’s average price per head for a 550 pound, Medium and Large Frame, Number 1 Muscle steer at the Joplin and Springfield markets.  That average amounted to $1011 per head according to the Missouri Market Summary.
The SMS heifer average of $2477 divided by the steer average resulted in a 2.45:1 figure.  In the previous sales the highest ratio was 2.4:1.  Since the SMS sales began in 1997 at Joplin the smallest ratio was 1.65:1 in 1999.
There was a standing room only crowd at the sale along wit…

Hereford Education Forum: AHA Developments in National Cattle Evaluation

Dorian Garrick
Iowa State University

The Pre-Genomic Era In the Pan-American Evaluation there are four countries, US, Canada, Uruguay and Argentina. Agricultural Business Research Institute (ABRI) collects the pedigree and trait data. Then the Animal Genetics & Breeding Unit uses BREEDPLAN to estimate EPDs.

To put the number of records turned in to the AHA data in context, we can compare them to other breeds. The 11 breed associations in International Genetic Solutions add 340,000 new animals in each of 2012 and 2013. AGI adds about 300,000 per year. Herefords add a little less than 100,000 animals per year.

The Early-Genomic Era Cattle have 30 pairs of chromosomes. There are about 100 million base pairs per chromosome and about 2.6 billion base pairs in the entire DNA (genome).

Most errors in chromosome replication are fixed. But, some slip through and are passed down through generations.

The EPD of a bull is a sum of the average gene effects he carries. Until the genomic era, we …

Hereford Educational Forum: New Traits

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Bill Bowman and Sally Northcutt
Method Genetics LLC

Bowman and Northcutt discussed several new EPDs either in development or released by AHA, including:

Dry Matter IntakeSustained Cow FertilityHeifer Calving RateUdder Quality (Teat Size and Udder Suspension)
Heifer Calving Rate, Sustained Cow Fertility, and Dry Matter Intake are currently released as prototype evaluations and can be accessed as a downloadable Excel file.

"One of the things you all have going for you is the foresight to begin a TPR program," said Bowman.

Heifer Calving Rate Heifer Calving Rate (HCR) is a categorical trait, they either calved or they didn't. Method Genetics reports a heritability of 15% for Heifer Calving Rate. They analyzed 98,000 records, of which 73% had calved by 800 days of age, 27% had not calved. Contemporary grouping for heifers is based upon their herd, yearling weigh date, calf birth year and season.

"This EPD goes beyond a traditional heifer pregnancy EPD." said Northcutt…

Angus Genetics Inc. Updates to EPD/Pedigree Lookup

Based on input and requests from breeders, we’ve been working on some updates to the information displayed on the Animal Search feature on Angus.org. These new features went live this morning [10 November 2015], and I want to take a minute to highlight and explain these enhancements.
Genomic Progeny EPD percentile ranksProgeny  For complete post, please visit Angus Genetics Inc blog, and read the post by Dr. Tonya Amen.
Decker's Take Home: I always love to see breed associations changing and innovating. I think these changes will allow producers to more quickly evaluate an animal's genetic merit. Plus, I'm sure breeders appreciate AGI responding to requests.

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The Power of the Genome: Weighing Opportunities, Dangers and Responsibility

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Angus Convention 2015
Richard Resnick
CEO of GenomeQuest

One can not impede scientific progress. - Mahmoud Ahmadinejad Resnick gave a series of examples of how genomics is changing society.

Resnick put a nice spin on the typical sequencing cost figure. He overlays Illumina's ($ILMN) stock price on top of the figure.

He went on to explain that the only real differences between humans, cattle, corn, and other species is the proteins they make. The amino acids, the building block of proteins, are actually the same between species.

Resnick used cystic fibrosis as an example of a disease in which genetics has been very important. One DNA variant that causes the disease is called ΔF508. When a person has this variant, the gene produces the protein, but a check and balance in the cell recognizes the protein as not correct and destroys it. A different variant, G551D, is not so severe that the protein is destroyed, but the protein does not function properly. A drug called Kalydeco alters the…

Forty-Nine Performance Bulls Average $4581 at the 86th Southwest Missouri Beef Cattle Improvement Association’s Bull Sale

Eldon Cole, Livestock Specialist
The 86th Southwest Missouri Beef Cattle Improvement Association’s bull sale averaged $4581 on 49 bulls.  Leading the average were the 46 Angus bulls that made $4684.  Three Polled Herefords were harder to get bids on and each received a $3000 bid.
The consignment had outstanding performance data behind them and the knowledgeable bidders on the seats found the top prospects throughout the sale.  One thing that stood out again was the reluctance of buyers to go very high on bulls that had calving ease direct expected progeny differences (EPD) that were poorer than breed average.
The sale top of the evening was a May, 2014 Angus consigned by Truman L. Wiles, Willow Springs.  The bulls calving ease, weaning weight and yearling weight ranked him in the first percentile for Angus non-parent bulls.  His $Wean was also in the first percentile.  The 7-framebull brought $7000 from Kevin and Cheryl Dill of Niangua.
Close behind at $6750 was the entry from Blue M…

Summary of the DNA Technology: Where we've been, where we are, and where we're headed Conference

Meat Animal Research Center, Clay Center, NE Matt Spangler
University of Nebraska-Lincoln
 Why are we working on these novel traits?
 Because they have great economic importance.
 Further, they have heritable genetic variation.

 We do have EPDs for feed intake and fertility, but they are not as pervasive as other (weight and carcass) traits.

Continued phenotypic data collection and recording is critically needed. But, the breed associations have to do something with the data. Otherwise, progressive seedstock producers will look outside breed associations for genetic evaluations. This will not be a great outcome for commercial cattle producers.

Nine breeds are already incorporating genomic information into EPD, with many other breeds right on the cusp of releasing genomic-enhanced EPDs.

As genotyping becomes more common and more animals are genotyped, many of the current limitations are eliminated. But, there is continued room for statistical approaches to be refined.

 Genotyping entir…

Selection for Improved Feed Efficiency

DNA Technology: Where we've been, where we are, and where we're headed
Conference sponsored by the Beef Feed Efficiency grant, beefefficiency.org Meat Animal Research Center, Clay Center, NE Matt Spangler
University of Nebraska-Lincoln
In poultry, we have seen a 250% improvement in feed efficiency since 1957. We have dramatically improved the efficiency of gain in chickens.

We have not made similar progress in beef cattle. How can we move the needle and start to make progress?

First of all, how do we define feed efficiency?

Average daily gain (ADG)Average daily feed intake (AFI)Residual feed intake (RFI) is the difference between what we expected an animal to eat and what they actually ate. In residual feed intake, how we define a contemporary group is very important. For example, think of combining Scottish Highland and Chianina cattle in a group. 

EPDs for feed efficiency

Residual gainresidual feed intakedray matter intakeDays to finish

If a breed publishes multiple efficiency …

Selection for Cattle that are Less Susceptible to BRD

DNA Technology: Where we've been, where we are, and where we're headed
Conference sponsored by the Beef Feed Efficiency grant, beefefficiency.org Meat Animal Research Center, Clay Center, NE
Alison Van Eenennaam
University of California-Davis
Twitter: @biobeef
The long-term goal of this project is to reduce the incidence of bovine respiratory disease (BRD) complex through genomic selection. We would not want to challenge our herd to see if they are susceptible or not; too many would end up dead! Genomics helps us select for traits that are difficult to measure or have a low heritability.

But to create genomic predictions we need large populations, e.g. 1000s of animals, with phenotypes (trait measurements) and genotypes. BRD can be difficult to measure and quantify; the data can be noisy. Part of the focus of the project was a very careful definition of a sick animal. Temperature, cough, nasal drainage, eye scores, and ear scores were used to define whether or not an animal was …

Selecting for More Fertile Females

DNA Technology: Where we've been, where we are, and where we're headed
Conference sponsored by the Beef Feed Efficiency grant, beefefficiency.org Meat Animal Research Center, Clay Center, NE Jared E. Decker
University of Missouri
Introduction It has frequently been stated that reproductive traits have low heritabilities, meaning little of the variation in reproductive traits is due to genetic differences. Due to this catchphrase, producers may not emphasize reproductive traits in their breeding decisions. Further, cows and heifers may sometimes receive a “Get Out of Jail, Free” card when their reproductive performance is lacking.
Let us reconsider the amount of variation in reproductive traits due to genetics. First consider the Heifer Pregnancy EPD reported by the American Angus Association. They report a heritability of 14% for Heifer Pregnancy (https://www.angus.org/Nce/Heritabilities.aspx ). At first, this may seem like a very small percentage. But, to put it in further pers…

Speaker Sensation at the National Angus Convention

Entertaining and educational, an impressive line-up headlines Angus events Nov. 3-5 in Overland Park, Kan.



The complete program for the 2015 Angus Means Business National Convention & Trade Show, which takes place Nov. 3-5 in Overland Park, Kan., features an incredible slate of speakers.

Highlights of the week’s events include an International Angus Genomics Symposium on Tuesday, Nov. 3, sponsored by Neogen®’s GeneSeek Operations, during which keynote speaker and genetics pioneer Richard Resnick will discuss the evolving progress of genomic technology. The afternoon will provide hands-on Genomics Innovation Workshops sponsored by Zoetis.

On Wednesday, Nov. 4, Angus University, sponsored by Merck Animal Health, returns to follow “A Story of a Steak” and share insights on increasing quality in the nation’s beef production chain. Ken Schmidt, former Harley-Davidson communications director is the morning keynote speaker. The afternoon will feature 21 educational breakouts with emphasi…

What have we learned from sequencing efforts to date?

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And where are we going next?
This graph never ceases to amaze me. On the horizontal axis we have dates from September 2001 to July 2015. On the vertical axis we have the cost to sequence a million base pairs of DNA, with the axis having a logarithmic scale (each tick mark is multiplied by 10, e.g. change from 10 to 100 to 1000). The blue line describes what is called Moore's Law which describes the increase in purchasing power as computer costs come down. The rate of improvement in DNA sequencing easily outpaces the improvement in computing. Since September 2001, the price of DNA sequencing has dropped 6 orders of magnitude from $5,292.39 to $0.015. From more than $5,000 to less than 2 cents!!!

What caused the drop in sequencing from April 2015 to July 2015? This is due to the release of the Illumina HiSeq X Ten system. Previously this system was only licensed for human sequencing. But on October 6th, this restriction was lifted and this system is now available for livestock geno…

2015 NBCEC Brown Bagger Series Kicks Off

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The 2015 National Beef Cattle Evaluation Consortium Brown Bagger series kicked off today. The Brown Bagger is a webinar discussing beef cattle genetics every Wednesday in October at 12:00 Central time. While we've already missed today's webinar, no fear there are more great presentations coming up. Plus, recordings of today's webinar will be available online in the coming weeks.

The theme for this year's series is "Advancing genetic selection in beef cattle: Improving current tools and developing new ones."

The following presentations are scheduled:

Oct 7 Advancements in National Cattle Evaluation Strategies
Host, Dr. Matt Spangler

Latest changes to national cattle evaluation systems—Dr. Bob Weaber, Kansas State UniversityAcross Breed EPD and multi-breed genetic evaluation developments—Dr. Larry Kuehn, USDA-ARS-US-Meat Animal Research Center

Oct 14 Beef Cattle Fertility Project and Sequencing Effort Update
Host, Dr. Darrh Bullock

Update on USDA Fertility Project—D…

MU Thompson Research Center event shows new beef genomics, AI breeding

Duane Dailey
Senior Writer, University of Missouri

SPICKARD, Mo. - It has happened before, but always surprises. The biggest, best-looking beef cows had the worst genetic scores.

At the University of Missouri Thompson Farm Field Day, eight cows were sorted out for study by farm visitors. Four cows were top of the herd. Four were on the bottom.

They were sorted on genetic value scores from DNA testing. Cows that looked the best to visitors who didn't know the scores were large frame in good condition, but their calves at side were light-muscled and less fleshy.

Jared Decker, MU Extension geneticist, said the bottom-scoring cows were ready to "go on down the road." They will be replaced by heifers from high-scoring younger cows.

The soon-to-be cull cows had not produced prime-grade calves like the high-scoring cows, Decker said.

Farm manager Jon Schreffler agreed with results from the GeneMax Advantage tests. The high-scoring cows also had high scores in herd records he ke…

Missouri Red Angus Association Creates Centralized Bull Test

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The Missouri Red Angus Association invites all Red Angus breeders large and small, near and far, to participate in a newly established bull test. Come and join the new era of the Missouri Red Angus Association.

Missouri Red Angus Association’s (MORAA) Board of Directors has been evaluating the past methodology for marketing bulls at the April MORAA sale in Springfield. Based on their evaluation and consistent member feedback that the old program was inadequate, a new program has been launched. The board believes this will be an excellent marketing opportunity for Red Angus genetics.

For cattlemen who have an interest in participating in the project, the test is now accepting entries with receiving dates from Oct. 1–15 for bulls born January, February and March of 2015.

Entry-Consignment Fee:
$200 per bullPaid at entry to the selected developerConsignor must be a current Missouri Red Angus member

Approved Test Facilities & Developers:
Green Springs Bull Test - Nevada, MO (Kent Abele

The Random Shuffle of Genes: Putting the E in EPD

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Please see the fact sheet for more information about the random shuffle of chromosomes and genes that happens between generations. This random shuffle explains the differences between full siblings, e.g. flush mates, and the low reliability of traditional EPDs for young animals.